Table 3 Comparison of scRNAbox’s usability and capabilities to the most relevant scRNAseq analysis tools currently available. Not available: the answer to this question remained uncertain after addressing the tool’s user manual and publication. Abbreviations: DGE, differential gene expression; HTO, oligonucleotide tagged Hashtag antibodies

Usability

Does it run on HPC automatically

Yes

No

No

No

No

No

No

No

No

No

No

Is it a web application

No

No

No

No

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Easy to use by wet-lab biologists

Yes

Yes

No

No

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Adaptable parameters

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Outputs intermediate objects for bioinformaticians

Yes

Yes

Yes

Yes

No

Yes

No

No

Yes

No

Yes

Extensive detailed documentation

Yes

Yes

Yes

Yes

Yes

No

Yes

Yes

Yes

No

Yes

Generatates visualization and numeric outputs

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Automatic pipeline to run all steps

Yes

Yes

No

No

No

No

No

No

No

Yes

No

Interactive pipeline to check each output

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

No

Yes

Data input

Takes in FASTQ files

Yes

Yes

No

No

No

No

No

No

No

No

No

Processes multiple samples in parallel

Yes

Yes

No

No

No

No

No

No

No

No

No

Takes in count matrices (CellRanger outputs)

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Takes in Seurat objects

Yes

No

Yes

No

No

No

No

No

No

No

No

Quality control and filtering

Ambient RNA detection and adjustement

Yes

No

No

No

No

No

No

No

No

No

No

Doublet detection and filtering

Yes

No

Yes

Yes

No

No

No

No

No

Yes

No

Filtering by unique/total RNA

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

yes

Yes

Filtering by percent mitochondrial DNA

Yes

Yes

Yes

Yes

yes

Yes

No

Yes

Yes

No

No

Filtering by percent ribosomal DNA

Yes

Yes

Yes

Yes

No

Yes

No

Yes

Yes

No

No

Filter out gene lists

Yes

No

Yes

Yes

No

No

Yes

No

Yes

Yes

No

Filter out cell cycle genes

Yes

No

Yes

Yes

No

No

Yes

No

Yes

Yes

No

Regress out gene lists

Yes

No

Yes

Yes

No

No

No

No

Yes

No

No

Sample Integration

Option to integrate samples

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Not available

Yes

No

No

Option to integrate separatetely processed samples from independent experiements

Yes

Yes

Yes

Yes

No

No

No

No

No

No

No

Clustering

Does clustering using Seurat

Yes

No

Yes

No

Yes

No

No

Yes

Yes

Yes

Yes

Allows tuning parameters for clustering and multple resolutions

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Calculates adjusted rand index to select optimal clustering outputs

Yes

No

No

No

No

No

No

No

No

No

No

Cluster annotation

Calculates intercluster DGE to find cluster markers

Yes

Yes

Yes

Yes

Yes

Yes

No

Yes

Yes

Yes

Yes

Gene enrichment analysis of cluster markers in cell type libraries

Yes

No

Yes

Yes

Yes

No

Yes

Yes

Yes

No

Yes

Calculates aggregated expression of user-defined gene sets

Yes

No

Yes

Yes

No

No

No

No

No

No

No

Predicts annotations with reference data

Yes

No

Yes

Yes

No

No

No

No

No

No

No

Allows visualization of custom marker sets

Yes

Yes

Yes

Yes

Yes

Yes

Yes

No

Yes

No

Yes

Differential gene expression

Calculates DGE by user-defined clusters between user-defined variables

Yes

Yes

Yes

Yes

Yes

No

Yes

No

No

No

Yes

Provides pseudobulk DGE comparisons

Yes

No

Yes

Yes

No

No

No

No

No

No

No

HTO feature seq analysis

Supports feature seq files

Yes

Yes

Yes

Yes

No

No

No

No

No

No

No

Provides HTO demultiplexing

Yes

Yes

Yes

Yes

No

No

No

No

No

No

No